[2023-06-13 03:34:36,809] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:34:36,811] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:34:36,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg78ed8ab2-b8d2-4739-82c6-459ba52e7c3d/dqc_reference
[2023-06-13 03:34:38,182] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:34:38,183] [INFO] Task started: Prodigal
[2023-06-13 03:34:38,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg13a62c30-c41f-4d0d-bd4e-c605c1e3080c/GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:34:41,184] [INFO] Task succeeded: Prodigal
[2023-06-13 03:34:41,184] [INFO] Task started: HMMsearch
[2023-06-13 03:34:41,184] [INFO] Running command: hmmsearch --tblout GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78ed8ab2-b8d2-4739-82c6-459ba52e7c3d/dqc_reference/reference_markers.hmm GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:34:41,418] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:34:41,420] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg13a62c30-c41f-4d0d-bd4e-c605c1e3080c/GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-13 03:34:41,469] [INFO] Query marker FASTA was written to GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 03:34:41,469] [INFO] Task started: Blastn
[2023-06-13 03:34:41,469] [INFO] Running command: blastn -query GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ed8ab2-b8d2-4739-82c6-459ba52e7c3d/dqc_reference/reference_markers.fasta -out GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:34:42,534] [INFO] Task succeeded: Blastn
[2023-06-13 03:34:42,538] [INFO] Selected 8 target genomes.
[2023-06-13 03:34:42,538] [INFO] Target genome list was writen to GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 03:34:42,542] [INFO] Task started: fastANI
[2023-06-13 03:34:42,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a62c30-c41f-4d0d-bd4e-c605c1e3080c/GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:34:45,275] [INFO] Task succeeded: fastANI
[2023-06-13 03:34:45,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78ed8ab2-b8d2-4739-82c6-459ba52e7c3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:34:45,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78ed8ab2-b8d2-4739-82c6-459ba52e7c3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:34:45,283] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:34:45,283] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 03:34:45,283] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Gardnerella swidsinskii	strain=GS 9838-1	GCA_003397705.1	2792979	2792979	type	True	86.073	306	372	95	below_threshold
Gardnerella leopoldii	strain=UGent 06.41	GCA_003293675.1	2792978	2792978	type	True	85.8965	303	372	95	below_threshold
Gardnerella vaginalis	strain=DSM 4944	GCA_900105405.1	2702	2702	suspected-type	True	82.5534	220	372	95	below_threshold
Gardnerella piotii	strain=UGent 18.01	GCA_003397585.1	2792977	2792977	type	True	82.3236	228	372	95	below_threshold
Gardnerella vaginalis	strain=ATCC 14018	GCA_000178355.1	2702	2702	suspected-type	True	82.157	193	372	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 03:34:45,286] [INFO] DFAST Taxonomy check result was written to GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 03:34:45,287] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:34:45,287] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:34:45,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78ed8ab2-b8d2-4739-82c6-459ba52e7c3d/dqc_reference/checkm_data
[2023-06-13 03:34:45,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:34:45,308] [INFO] Task started: CheckM
[2023-06-13 03:34:45,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 03:35:04,860] [INFO] Task succeeded: CheckM
[2023-06-13 03:35:04,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:35:04,891] [INFO] ===== Completeness check finished =====
[2023-06-13 03:35:04,892] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:35:04,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 03:35:04,892] [INFO] Task started: Blastn
[2023-06-13 03:35:04,892] [INFO] Running command: blastn -query GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ed8ab2-b8d2-4739-82c6-459ba52e7c3d/dqc_reference/reference_markers_gtdb.fasta -out GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:35:05,483] [INFO] Task succeeded: Blastn
[2023-06-13 03:35:05,487] [INFO] Selected 9 target genomes.
[2023-06-13 03:35:05,487] [INFO] Target genome list was writen to GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:35:05,502] [INFO] Task started: fastANI
[2023-06-13 03:35:05,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a62c30-c41f-4d0d-bd4e-c605c1e3080c/GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:35:09,092] [INFO] Task succeeded: fastANI
[2023-06-13 03:35:09,101] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 03:35:09,101] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_003585735.1	s__Bifidobacterium sp003585735	94.5787	353	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	99.73	99.73	0.99	0.99	2	-
GCF_000263635.1	s__Bifidobacterium vaginale_C	88.6793	323	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	96.53	95.52	0.94	0.93	5	-
GCF_000263595.1	s__Bifidobacterium vaginale_E	87.9564	324	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	95.68	95.61	0.91	0.90	4	-
GCA_003585845.1	s__Bifidobacterium sp003585845	86.2191	319	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	N/A	N/A	N/A	N/A	1	-
GCF_001546485.1	s__Bifidobacterium vaginale_D	86.132	298	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	98.87	98.82	0.95	0.94	3	-
GCF_003408845.1	s__Bifidobacterium vaginale_H	86.1249	292	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003397705.1	s__Bifidobacterium swidsinskii	86.029	308	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.6629	98.35	97.96	0.94	0.90	18	-
GCF_003293675.1	s__Bifidobacterium leopoldii	85.8666	304	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.706	98.89	98.40	0.95	0.92	16	-
GCF_002896555.1	s__Bifidobacterium vaginale_F	83.8543	232	372	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 03:35:09,112] [INFO] GTDB search result was written to GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 03:35:09,113] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:35:09,128] [INFO] DFAST_QC result json was written to GCA_947253155.1_SRR17635716_bin.2_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 03:35:09,128] [INFO] DFAST_QC completed!
[2023-06-13 03:35:09,128] [INFO] Total running time: 0h0m32s